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- PDB-1t6t: putative protein from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 1t6t
Titleputative protein from Aquifex aeolicus
Componentsputative protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Aquifex aeolicus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyRibonuclease M5-like, TOPRIM domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / TOPRIM / Toprim domain / TOPRIM domain / 3-Layer(aba) Sandwich / Alpha Beta / Toprim domain-containing protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: putative protein from Aquifex aeolicus
Authors: Cuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: putative protein
2: putative protein


Theoretical massNumber of molelcules
Total (without water)27,6712
Polymers27,6712
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.906, 58.405, 54.124
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative protein


Mass: 13835.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: NP_214428 / Production host: Escherichia coli (E. coli) / References: UniProt: O67859
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ethanol, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 21, 2003 / Details: SBC2
RadiationMonochromator: sagitally focussed Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.8→26.73 Å / Num. all: 22463 / Num. obs: 22463 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.9 Å2 / Limit h max: 22 / Limit h min: -24 / Limit k max: 29 / Limit k min: -24 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 843216.03 / Observed criterion F min: 6.5
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.7 / % possible all: 43.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→26.73 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1117 5 %RANDOM
Rwork0.18 ---
all0.181 26335 --
obs0.181 22463 85.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 76.684 Å2 / ksol: 0.415027 e/Å3
Displacement parametersBiso max: 68.25 Å2 / Biso mean: 24.64 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å2-1.19 Å2
2--1.19 Å20 Å2
3---1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 395 2198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg20.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.59
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.226845.90.21813500.0253275143443.8
1.88-1.980.26914.60.20419030.0273271199460.9
1.98-2.110.2131304.30.17628790.0193284300991.6
2.11-2.270.2341635.10.17630260.0183288318997
2.27-2.50.2121865.80.17730080.0163275319497.5
2.5-2.860.2381524.70.18930900.0193311324297.9
2.86-3.60.1971745.40.17230610.0153290323598.3
3.6-26.730.1771374.30.17830290.0153366316694
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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